OpenMM Zephyr
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OpenMM Zephyr has been deprecated. We invite you instead to explore the OpenMM Script Builder web application, which provides a similar functionality. With pull-down menus and error checking, you can easily generate a script to run your simulation on OpenMM. Access the OpenMM Script Builder at http://builder.openmm.org. Read more about the OpenMM Script Builder and running scripts within OpenMM in Chapter 4 of the OpenMM Users' Guide at http://openmm.org. The current release of OpenMM Zephyr enables acceleration of molecular dynamics on specific NVIDIA and ATI GPU cards and operating systems. To find out if your NVIDIA or ATI GPU is supported please see the Documentation Links section of the OpenMM Zephyr package. Need help? See the discussion forums (Advanced -> Public Forums) Citing: Please cite this website https://simtk.org/home/zephyr in any published work which utilizes OpenMM Zephyr
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0penMM Zephyr
Graphical user interface for running OpenMM version of Gromacs. To use Zephyr's visualization capabilities, you will also need to install VMD (optional but recommended).
Zephyr 2.0
Jul 08, 2010

Based on OpenMM 2.0. CUDA and OpenCL support provided. Explicit solvent simulations supported. NOTE: Due to ATI's implementation of OpenCL, GPU acceleration of explicit solvent simulations is only possible on their HD5000 series boards.Notes  View License

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PLEASE CITE THESE PAPERS

P. Eastman and V.S. Pande. "OpenMM: A Hardware-Independent Framework for Molecular Simulations." Computing in Science & Engineering, 12:34-39. (2010)

M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, V. S. Pande. “Accelerating Molecular Dynamic Simulation on Graphics Processing Units.” J. Comp. Chem., 30(6), 864-872. (2009) View

Please cite: this code was made freely available on https://simtk.org/home/zephyr by the Simbios NIH National Center for Biomedical Computing. Simbios is supported by the National Institutes of Health through the NIH Roadmap for Medical Research Grant U54 GM072970 (2009)

ADDITIONAL PAPERS

P. Eastman and V.S. Pande. "Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations." J. Chem. Theor. Comput. 6:434-437. (2010)

P. Eastman and V.S. Pande. "Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit." J. Comput. Chem. 31:1268-72. (2010)


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Additional GPL source code
Source code for Gromacs and FFTW binaries used in Zephyr, made available under GPL license.
Gromacs and FFTW for Zephyr 0.8
Jun 09, 2009

  

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Christopher Bruns
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Russ Altman
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Vijay Pande

SimTK is maintained through Grant R01GM124443 01A1 from the National Institutes of Health (NIH). It was initially developed as part of the Simbios project funded by the NIH as part of the NIH Roadmap for Medical Research, Grant U54 GM072970.

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